RECOMMENDATIONS/PREREQUISITES:

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1 MODULE: MODULE NUMBER: JACS CODE: Biochemical Skills II BIO00001I C700 STAGE / YEAR: CREDITS: 30 ORGANISER: SUBJECT COMMITTEE: Dr Christoph Biochemistry VERSION: October 015 TERMS TAUGHT: Aut/Sp/Su 015/16 RECOMMENDATIONS/PREREQUISITES: Modules BIO00004C and BIO00008C, or equivalent modules. Good understanding of algebra, basic statistics and linear regression, and how to input data into a computer, e.g. how to copy a file, how to access a pull down menu, etc. SUMMARY: The polymerase chain reaction (PCR) is perhaps the most important innovation in molecular biology since the introduction of DNA sequencing and the use of plasmids and restriction enzymes. PCR is used widely in gene cloning, mrna quantification, DNA subcloning and site directed mutagenesis, diagnostic techniques in forensic and clinical studies, as well as in molecular evolution and population genetics. The lectures and practicals on molecular methods (Autumn term) will introduce students to some of the applications of PCR, PCR primer design and DNA sequencing. The lectures and workshops on modelling biochemical dynamics (Part A, Spring term) will train students in some key techniques for mathematical modelling and programming. Students will learn how to implement these techniques in MATLAB. In addition, students will gain experience of group working and of undertaking and presenting interdisciplinary work. There will be training in project management; developing, criticising and implementing computational and mathematical models; and oral and written presentation. In the section on biochemical and biophysical methods (Part B, Spring term), students will be introduced to the physical approaches used to characterise protein protein, protein DNA and protein ligand interactions in a modern biochemical laboratory. Two introductory lectures

2 (L1B LB) will cover the challenges involved in investigating biomolecular interactions. The remaining sessions (L3B L10B) will be delivered as interactive problem solving workshops where students will apply what they have learned through structured independent study. Students will have access to online learning materials covering the following: analytical ultracentrifugation and molecular weight determination, gel electrophoresis mobility assays, detection and characterisation of protein ligand interactions, ultraviolet and visible spectroscopies, fluorescence spectroscopy and techniques for studying molecular interactions at the single molecule level. The module will conclude (weeks 1 3, Summer term) with a mini project using C. elegans nematode worm to investigate chemotaxis behaviour. A series of lectures and practicals will introduce chemosensory behaviour in C. elegans and some techniques used to study this organism. Key concepts in experimental design, data analysis, critical reading of the literature, and research poster design will be reinforced in the lectures and workshops. These concepts will be applied in the student directed mini project. LEARNING OUTCOMES: How to set up a PCR and use of a thermocycler To learn how to use PCR for gene expression studies (such as RT PCR and Q PCR) To inform about the parameters that are critical for successful PCR, and to confer the ability to design oligonucleotide primer To provide knowledge of automated DNA sequencing, including next generation sequencing technologies, and to introduce the use of computer programmes for DNA sequence analysis To understand and to have experience of key elements of algorithmic programming using MATLAB To understand and to have experience of the key biological, mathematical and computational elements involved in modelling biological and biochemical systems To be able to understand the key elements of differential equation models for biological dynamics, e.g. linear interactions (leading to exponential dynamics), nonlinear interactions, inter and intra processes To have experience of interdisciplinary group work, including delegation of tasks and time management, and presentation of results To introduce the physical approaches used to characterise protein protein, protein DNA and protein ligand interactions in present day biochemical research To confer a sound understanding of the theoretical principles and some of the practice underlying the following techniques: analytical ultracentrifugation, ultraviolet and visible spectroscopies, fluorescence spectroscopy, and gel electrophoresis mobility assays To learn how to use quantitative data analysis to extract parameters describing binding equilibria

3 To provide knowledge of chemosensory behaviour in C. elegans and some techniques used to study this organism To practice critical reading of the literature, experimental design, problem solving and quantitative data analysis SYNOPSIS OF TEACHING: Event Duratio n (hrs) Topic Staff Room type Timing AUTUMN TERM Tutorial s 6 x 1h The tutorials will cover research topics selected by the students. These tutorials will involve critical reading of scientific papers, oral presentations, and preparation of an extended essay. Tutors will schedule these tutorials to accommodate the students timetables. Various Lecturers office PCR applications and DNA sequencing L1 1 Introduction to PCR and an overview of practicals 1 3 P1 Setting up reverse transcription PCR (RT PCR) P 3 Gel electrophoresis of RT PCR products. Setting up real time PCR. P3 3 Q PCR analysis (computer session) L Introduction to DNA Sequencing and Sequence Analysis. This includes an Schultze Wk, ideally Monday Schultze Biolabs Wk, AM if possible Schultze Biolabs Wk, AM session essential Schultze A004 Wk 3 Schultze Wk 4 ideally one

4 overview on new sequencing technologies (454 pyrosequencing, Illumina, IonTorrent, Pacific Biosciences single molecule real time sequencing, nanopore sequencing) day before P4, not on the same day as P4. DNA sequencing: Schultze Biolabs Wk 4 P4a P4b P4c 1 4 x 0 min P4a DNA sequencing reactions P4b Demonstration of DNA sequencing and quantitative PCR (Q PCR) equipment in TF a) AM session 1 hour b) Genomics lab demo (around lunch time) 1.5 h split in 0 min per 14 students P4c Precipitation of DNA c) at least h gap between 4a and 4c, hours P5 3 DNA sequence analysis (computer session) L3 1 Principles of PCR Primer Design P6 3 PCR primer design lab (computer session) L4 1 Debriefing of the practical sessions. Discussion of results obtained. Schultze A004 Wk 5 must allow minimum work days after session P4 Schultze Wk 6 Must come before P6 Schultze A004 Wk 6 Schultze Not later than Wk 7 W1 1 Careers session entitled: " Finding and making the most of work experience " Ungar, Janice Simpson Wk 9, timetabled jointly for Biochemistry and Biology UG students

5 SPRING TERM Tutorial s 6 x 1h The tutorials will cover research topics selected by the students. These tutorials will involve critical reading of scientific papers, oral presentations, and preparation of an extended essay. Tutors will schedule these tutorials to accommodate the students timetables. Various Lecturers office Part A Modelling Biochemical Dynamics L1A 1 Differential equations (ODEs) an introduction LA 1 Elements of ODEs 1: linear processes and exponential growth, nonlinear processes and logistic limitation (link to W) L3A 1 Elements of ODEs : extending to more than one dimension and simple linear interactions L4A 1 Elements of ODEs 3: nonlinear interactions, Michaelis Menten, Hill and Holling I III functions and switches L5A 1 Preparation for group project work: requirements, methods, planning and reporting Pitchford joint with 3I MBD module cohort Pitchford before W, joint with 3I MBD module cohort Pitchford joint with 3I MBD module cohort Pitchford joint with 3I MBD module cohort Pitchford joint with 3I MBD module cohort W1 Introduction to MATLAB: variables, vectors, matrices, loops and functions. Pitchford A004

6 W Simple exponential and logistic dynamics using Euler s method and ODE45 W3 Lotka Volterra predator prey and competition dynamics W4 Nonlinear dynamics in biochemical reactions (enzyme kinetics and inhibition) Pitchford A004 after LA Pitchford A004 after L3A Pitchford A004 after L4A Support ed learning session Help session students have the opportunity to utilise MATLAB for P1 data analy sis Pitchford, A004 after P1 in Part B Semina r session 3 Group presentations on biochemical modelling problem (assessed) Pitchford, (B00, B006 or K018) minimum of 4 days after Supported learning session 1 Support ed learning session Help session students have the opportunity to utilise MATLAB for P data analysis Pitchford, A004 after P in Part B Part B Biochemical and Biophysical Methods L1B 1 Introduction to investigating molecular interactions LB 1 Introduction to investigating molecular interactions L3B 1 Detection and characterisation of oligomerisation L4B 1 Detection and characterisation of protein/nucleic acid interactions

7 L5B 1 Detection and characterisation of protein ligand interactions L6B 1 Spectroscopic techniques: theory and practice L7B 1 Ultraviolet spectroscopy before P1 P1 3 Ultraviolet spectroscopy lab Biolabs L8B 1 Fluorescence spectroscopy before P L9B 1 Fluorescence spectroscopy before P P 3 Fluorescence spectroscopy lab L10B 1 Studying molecular interactions at the single molecule level Biolabs L11B 1 Introduction to the biology of C.elegans, and chemosensory behaviour in worm. Chong, S Wk 10 L1B 1 Experimental design and methods. A series of approaches to tackle problems will be covered in this lecture. Wk 10 after L11B SUMMER TERM Tutorial s x 1h Tutors will provide detailed feedback on the extended essay prepared during Spring term. Tutors will schedule these tutorials to accommodate the students timetables. Various Lecturers offices P1 Students will be introduced to methods of handling C.elegans and shown how to distinguish and recognise worms in different developmental stages Biolabs Wk

8 P Students will gain further experience applying the skills and knowledge acquired in P1 Biolabs Wk W1 Students will design their chemotaxis experiments and organise required reagents. Students will set criteria for peer assessment of individual contributions to group work. Biolabs Wk 1 Mini pro ject week open lab period Set up chemotaxis plates and observation of chemotaxis behaviour. Collection and analysis of data, and redesigning of experiments ( weeks open lab period). Weekly meetings will be scheduled with the practical organiser to discuss student progress and data analysis. Biolabs Wks 3 W How to design a poster (computer session) Roberts Phil, A004 Wk 3 W3A W3B Help session and student progress meetings Biolabs Wk W3C W4A W4B Help session and student progress meetings Biolabs Wk 3 W4C W5A W5B Help session and student progress meetings Biolabs Wk 4 Support ed learning 1 Summary of the main topics/themes in the module; students will have the opportunity to ask questions Wk 4

9 session about material covered in the module. W6A W6B Help session and data analysis support Biolabs Wk 8 All day Poster Session Assessment All day Tuesday Week 9 of the Summer term. ChongS, White, Moir,, Chong J, Thomas G,, Potts, Biolabs Wk 9 W7 1 Feedback session on group poster presentations Wk 9 after poster session assessment Students are expected to work in groups of two in the practical sessions and individually in the computer sessions. Students will work in groups of 4 5 during the mini project. LECTURERS: Christoph (CGB), James Chong (JPJC), Setareh Chong (SSC), James Moir (JM), Michael (MP), Jon Pitchford (JWP), Jen Potts (JP), Phil Roberts (PR), Michael Schultze (MS), Sean (STS), Gavin Thomas (GHT), Dani Ungar (DU), Bob White (RJW) KEY TEXTS : These are available in EARL, which is accessible through the VLE module site. ASSESSMENT : Formative: Yes via VLE Summative: 30% for open book closed exam (1 hour) 0% for write up on molecular methods (PCR and DNA sequencing only, Autumn term) 0% for lab notebook (due Monday of week in Summer term) 15% for group presentation on biochemical modelling problem 15% for the group poster/group viva on C. elegans mini project.

10 Re assessment: Yes, details to be supplied later. DEMONSTRATING REQUIREMENTS: Details supplied separately MAXIMUM NUMBERS: to capacity of lecture theatres/biolabs/computer lab STUDENT WORKLOAD: students workload totalling 100 hours per 10 credit module Lectures: 14 Workshops: 36 (assume each student attends optional workshops for 3 hr/wk in wks 3, and hr/wk in wks 4 and 8 of Summer term) Supported learning sessions: 5 Practicals: 4 Tutorials 14 Total Contact hours: 93 Mini project: 35 Assessments : 1 hr (formative) + 1 hr (summative) Private study: 17